Sponer Judit E, Leszczynski Jerzy, Sychrovský Vladimír, Sponer Jirí
Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
J Phys Chem B. 2005 Oct 6;109(39):18680-9. doi: 10.1021/jp053379q.
Cis and trans sugar edge/sugar edge (SE/SE) binding patterns are essential building units of RNAs. For example, SE/SE interactions form the A-minor motifs, the most important tertiary interaction type in functional RNAs. This study provides an in-depth structure and stability analysis for these two base pair families. Gas-phase-optimized geometries are reported for 12 cis and 7 trans SE/SE base pairs and contrasted to their X-ray counterparts. Interaction energies are computed at the RIMP2 level of theory using the density-functional-theory-optimized geometries. There is a good overall agreement between the optimized and X-ray geometries of the cis SE/SE base pairs. In contrast, only three of the seven trans SE/SE binding patterns could be optimized without a significant distortion of the X-ray geometry. Note, however, that many SE/SE base pairs participate in broader networks of interactions; thus it is not surprising to see some of them to deviate from the X-ray geometry in a complete isolation. Computed interaction energies reveal that all 12 known cis SE/SE binding patterns are very stable. Among the trans SE/SE binding patterns, only the rG/rG, rG/rC, and rA/rG base pairs are sufficiently stable in the crystal geometry. Prediction has been made for some structures not yet detected by crystallography, namely, cis rC/rC, rG/rC, rG/rU, and rU/rU and trans rG/rA base pairs. Interestingly, the new cis SE/SE binding patterns are not necessarily isosteric with the remaining 12 members of this family. The trans rG/rA base pair represents a viable option for base pairing in RNA to be identified by future X-ray studies. In a complete lack of structural information, prediction of other unknown members of the trans SE/SE family was not attempted. Analysis of the interaction energies shows a very large electron correlation component of the interaction energy, pointing at the elevated role of dispersion energy as compared to other types of base pairs. This likely is profitable for stabilization of SE/SE binding patterns in polar environments and could be one of the reasons why the A-minor motif is the leading type of tertiary interactions in RNAs.
顺式和反式糖边缘/糖边缘（SE/SE）结合模式是RNA的基本构建单元。例如，SE/SE相互作用形成了A- minor基序，这是功能性RNA中最重要的三级相互作用类型。本研究对这两个碱基对家族进行了深入的结构和稳定性分析。报道了12个顺式和7个反式SE/SE碱基对的气相优化几何结构，并与它们的X射线对应结构进行了对比。使用密度泛函理论优化的几何结构，在RIMP2理论水平上计算相互作用能。顺式SE/SE碱基对的优化几何结构与X射线几何结构总体上吻合良好。相比之下，七个反式SE/SE结合模式中只有三个能够在不显著扭曲X射线几何结构的情况下进行优化。然而，请注意，许多SE/SE碱基对参与了更广泛的相互作用网络；因此，看到其中一些在完全孤立的情况下偏离X射线几何结构并不奇怪。计算得到的相互作用能表明，所有12种已知的顺式SE/SE结合模式都非常稳定。在反式SE/SE结合模式中，只有rG/rG、rG/rC和rA/rG碱基对在晶体几何结构中足够稳定。对一些尚未通过晶体学检测到的结构进行了预测，即顺式rC/rC、rG/rC、rG/rU和rU/rU以及反式rG/rA碱基对。有趣的是，新的顺式SE/SE结合模式不一定与该家族的其余12个成员等排。反式rG/rA碱基对代表了RNA中碱基配对的一个可行选择，有待未来的X射线研究来确定。在完全缺乏结构信息的情况下，没有尝试预测反式SE/SE家族的其他未知成员。相互作用能分析表明，相互作用能中存在非常大的电子相关成分，这表明与其他类型的碱基对相比，色散能的作用增强。这可能有利于在极性环境中稳定SE/SE结合模式，并且可能是A- minor基序是RNA中主要的三级相互作用类型的原因之一。
